subset vcf to keep only samples heterozygous or homozygous for the alternate allele of a given variant
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3 months ago
curious ▴ 640

position 45094160 on chromosome 15 in my vcf of 100 samples corresponds to a missense variant

I want to create a new vcf that contains only those samples of the 100 that are homozygous or heterozygous for the alternate allele at pos 45094160. I realize that I can do this with python or grep with some work, but I am wondering if there is a handy way to do it with bcftools or some other high level tool using the position or ID?

Thanks.

bcftools • 272 views
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Entering edit mode
3 months ago
cfos4698 ▴ 490

If you want to use bcftools, you'll first need to get a list of all samples that are heterozygous or homozygous for the alternate allele in an initial step somehow, then use:

bcftools view -s sample1,sample2 file.vcf > filtered.vcf
bcftools view -S sample_file.txt file.vcf > filtered.vcf

(https://bioinformatics.stackexchange.com/questions/3477/how-to-subset-samples-from-a-vcf-file)

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